There are plenty of niggles when moving R5 apps to ND6, and to be honest, you'll only really find them with thorough testing. Generally you should find the move goes OK, but there are some things to look out for. FWIW, I've been keeping a running list of issues encountered either personally or by others in my organisation. I fyully expect this list to expand once we really get into the nitty gritty of ND6 testing:
Views can be edited by end-users (columns, order, etc.) for their own use. The flag allowing this is enabled by default when you move an R5 database in to an ND6 environment, which is a pain, so check it in any applications where this is going to be an issue.
There's a bug (as at 6.02CF1) whereby the properties & methods of a NotesView object, accessed using the NotesDatabase.GetView method can return an error. This occurs with "Private on first use" views and folders. See Knowledgebase document #1108323 (Using Method or Property of NotesView Object Returns Error: "Index Is not to Be Generated on Server") for more information.
Make sure that any bug work-arounds and general "hacks" are well-documented in your code as you move forward, and that you test them all: they may not be required in ND6, and could cause other issues.
Notes UI Classes
The front-end Lotusscript classes have been tweaked with this release; be especially vigilant with regards NotesUIWorkspace.Compose
code: test it and make changes as required.
Security options in agents have been beefed-up. Make sure you read the Domino Designer document highlighted below, and then make any changes you deem necessary:
"Setting up agent security using the Security tab"
Hotspots & tabbed tables
URL hotspots (haven't tested other types) embedded in tabbed table rows don't appear to work. Clicking on them results in the tabbed table being moved on a row, rather than opening the hotspot. Works fine in R5, but buggy in 6.0.1, 6.0.2 and 6.0.3 (see post by Matt Dickens in this forum).
Great idea, usual half-baked implementation: have not managed to get it to work properly on anything but the simplest of tasks
HTH: this is not by any means an exhaustive list, just issues that have had an impact for us. Searching this forum will yield plenty more stuff!